Functional Characterization of Maize C2H2 Zinc-Finger Gene Family

Wei, Kaifa; Pan, Si Yuan; Yang, Li

doi:10.1007/s11105-015-0958-7

Cited by 40 publications

(41 citation statements)

References 73 publications

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“…Here, the gene structures and motifs present were highly similar among members of the same C2H2-ZF groups (Figure 3 and 4); for example, the members of Groups I, II, and V had 3-5 exons (Figure 3), while the most complex arrangements of motifs were observed in Group II (Figure 4). These results were similar to those of previous analyses of the C2H2-ZF family genes in maize (Zea mays) (Wei et al, 2016), soybean (Yuan et al, 2018), andpoplar (Liu et al, 2015). Therefore, our results suggest that the sequences and biological functions of the C2H2-ZFPs were relatively conserved among members of the nine subgroups, indicating that our classification of the tomato C2H2-ZFPs was reasonable.…”

Section: Discussionsupporting

confidence: 91%

“…In this study, using 97 Arabidopsis C2H2-ZFP sequences as a query, we identified 104 C2H2-ZF family members in the tomato genome, which contains at least one C2H2-ZF motif (X2-Cys-X(2-4)-Cys-X12-His-X(3-5)-His), and the lengths of these sequences varied from 96 to 1,178 amino acid residues, with striking distinctions (Table S2), suggesting that a high degree of complexity among the tomato C2H2-ZFs (Liu et al, 2015). The 'QALGGH' motif was almost invariant in the tomato C2H2-ZFPs ( Figure 2); however, the C2H2-ZFP subfamilies in other plant species have previously been defined based on changes to the conserved "QALGGH" motif (Fedotova et al, 2017;Liu et al, 2015;Razin et al, 2012;Takatsuji, 1999;Wei et al, 2016;Yuan et al, 2018;Zhang et al, 2016). In this study, to reveal phylogenetic relationship of tomato C2H2 family members, 104 C2H2-ZFPs were divided into nine major groups according to the NJ phylogenetic tree ( Figure 1B), which were well consistent with arrangements, numbers, and types of their C2H2-ZF domains (Figure 2).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Peer Review #1 of "Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.) (v0.1)"

2019

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The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon-intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Peer Review #1 of "Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.) (v0.1)"

2019

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“…Only a few mutations in flowering time genes have been identified so far, which contributes to the lack of current understanding of genetic and regulatory factors that determine maize phenology. Our current knowledge about maize flowering time is mainly based on results from QTL meta-analysis, (transposon) mutagenesis, and comparative genomics studies with the Arabidopsis and rice genomes (Buckler et al, 2009; Wei et al, 2015). Key phenology genes are listed in Table 4 .…”

Section: Flowering Time In Cereal Crops: a Complex Interplay Between mentioning

confidence: 99%

Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

Hill

2016

Front. Plant Sci.

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Cereal crop species including bread wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), and maize (Zea mays L.) provide the bulk of human nutrition and agricultural products for industrial use. These four cereals are central to meet future demands of food supply for an increasing world population under a changing climate. A prerequisite for cereal crop production is the transition from vegetative to reproductive and grain-filling phases starting with flower initiation, a key developmental switch tightly regulated in all flowering plants. Although studies in the dicotyledonous model plant Arabidopsis thaliana build the foundations of our current understanding of plant phenology genes and regulation, the availability of genome assemblies with high-confidence sequences for rice, maize, and more recently bread wheat and barley, now allow the identification of phenology-associated gene orthologs in monocots. Together with recent advances in next-generation sequencing technologies, QTL analysis, mutagenesis, complementation analysis, and RNA interference, many phenology genes have been functionally characterized in cereal crops and conserved as well as functionally divergent genes involved in flowering were found. Epigenetic and other molecular regulatory mechanisms that respond to environmental and endogenous triggers create an enormous plasticity in flowering behavior among cereal crops to ensure flowering is only induced under optimal conditions. In this review, we provide a summary of recent discoveries of flowering time regulators with an emphasis on four cereal crop species (bread wheat, barley, rice, and maize), in particular, crop-specific regulatory mechanisms and genes. In addition, pleiotropic effects on agronomically important traits such as grain yield, impact on adaptation to new growing environments and conditions, genetic sequence-based selection and targeted manipulation of phenology genes, as well as crop growth simulation models for predictive crop breeding, are discussed.

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“…ATGs location on B. napus chromosomes was obtained from the Brassica database (BRAD) database [ 43 ]. Genes with a maximum interval of 10 genes on the same chromosome were regarded as tandem duplication [ 84 ]. Two criteria are considered to recognize segmental duplication, including more than 80% identification of the aligned region and more than 80% alignment coverage compared to the longer genes [ 85 ].…”

Section: Methodsmentioning

confidence: 99%

In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Eshkiki

Hajiahmadi

Abedi

et al. 2020

Plants

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The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.

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Functional Characterization of Maize C2H2 Zinc-Finger Gene Family

Cited by 40 publications

References 73 publications

Peer Review #1 of "Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.) (v0.1)"

Peer Review #1 of "Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.) (v0.1)"

Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

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